Discovery and mapping of genomic regions governing economically important traits of Basmati rice

BMC Plant Biology

Research Article

Sabahat Noor¹  VV Satyavathi¹  A Kaliappan¹  SRN Parimala¹  Javaregowda Nagaraju¹  KV Sudhakar Rao²  N Shobharani³  Prathibha M Bharathi⁴  Dondapati A Deborah⁴  EA Siddiq⁵  Lakshminarayana R Vemireddy⁵  A Srividhya⁵ 

[1] Centre for DNA Fingerprinting and Diagnostics, 500001, Hyderabad, India;Centre for DNA Fingerprinting and Diagnostics, 500001, Hyderabad, India;Indian Institute of Rice Research, Hyderabad, India;Indian Institute of Rice Research, Hyderabad, India;Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, 500030, Hyderabad, AP, India;Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, 500030, Hyderabad, AP, India;Centre for DNA Fingerprinting and Diagnostics, 500001, Hyderabad, India;

关键词: Basmati rice;    Quantitative trait loci;    Quality traits;    Microsatellite markers;    Non-synonymous SNPs;    Candidate genes;   

DOI  :  10.1186/s12870-015-0575-5

 received in 2015-05-20, accepted in 2015-07-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundBasmati rice, originated in the foothills of Himalayas, commands a premium price in the domestic and international markets on account of its unique quality traits. The complex genetic nature of unique traits of Basmati as well as tedious screening methodologies involved in quality testing have been serious constraints to breeding quality Basmati. In the present study, we made an attempt to identify the genomic regions governing unique traits of Basmati rice.ResultsA total of 34 Quantitative Trait Loci (QTLs) for 16 economically important traits of Basmati rice were identified employing F2, F3 and Recombinant Inbred Line (RIL) mapping populations derived from a cross between Basmati370 (traditional Basmati) and Jaya (semi-dwarf rice). Out of which, 12 QTLs contributing to more than 15 % phenotypic variance were identified and considered as major effect QTLs. Four major effect QTLs coincide with the already known genes viz., sd1, GS3, alk1 and fgr governing plant height, grain size, alkali spreading value and aroma, respectively. For the remaining major QTLs, candidate genes were predicted as auxin response factor for filled grains, soluble starch synthase 3 for chalkiness and VQ domain containing protein for grain breadth and grain weight QTLs, based on the presence of non-synonymous single nucleotide polymorphism (SNPs) that were identified by comparing Basmati genome sequence with that of Nipponbare.ConclusionsTo the best of our knowledge, the current study is the first attempt ever made to carry out genome-wide mapping for the dissection of the genetic basis of economically important traits of Basmati rice. The promising QTLs controlling important traits in Basmati rice, identified in this study, can be used as candidates for future marker-assisted breeding.

【 授权许可】

CC BY   
© Vemireddy et al. 2015